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ZhangGroup-MITChemistry · Mar 26, 2024 · 6083189 · 6083189
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diff --git a/docs/GettingStarted/Installation.html b/docs/GettingStarted/Installation.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Installation &mdash; openNucleome 1.1.0 documentation</title><link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+  <title>Installation &mdash; openNucleome 1.1.3 documentation</title><link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/jupyter-sphinx.css" type="text/css" />
       <link rel="stylesheet" href="../_static/thebelab.css" type="text/css" />
@@ -39,7 +39,7 @@
               <img src="../_static/website_pic.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                1.1.0
+                1.1.3
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -65,7 +65,7 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../Tutorials/LangevinSimulation.html">Sphere Model: Langevin Dynamics</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../Tutorials/BrownianSimulation.html">Sphere Model: Brownian Dynamics</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../Tutorials/NuclearDeformation.html">Ellipsoid Model: Nuclear Deformation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../Tutorials/NuclearDeformation.html">Nuclear Deformation Simulation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../Tutorials/ConfigsGeneration.html">Tutorials: Configuration Generation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../Tutorials/ConfigsRelaxation.html">Tutorials: Configuration Relaxation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../Tutorials/ConfigsSelection.html">Tutorials: Configuration Selection</a></li>

diff --git a/docs/GettingStarted/Introduction.html b/docs/GettingStarted/Introduction.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Introduction &mdash; openNucleome 1.1.0 documentation</title><link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+  <title>Introduction &mdash; openNucleome 1.1.3 documentation</title><link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/jupyter-sphinx.css" type="text/css" />
       <link rel="stylesheet" href="../_static/thebelab.css" type="text/css" />
@@ -39,7 +39,7 @@
               <img src="../_static/website_pic.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                1.1.0
+                1.1.3
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -62,7 +62,7 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../Tutorials/LangevinSimulation.html">Sphere Model: Langevin Dynamics</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../Tutorials/BrownianSimulation.html">Sphere Model: Brownian Dynamics</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../Tutorials/NuclearDeformation.html">Ellipsoid Model: Nuclear Deformation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../Tutorials/NuclearDeformation.html">Nuclear Deformation Simulation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../Tutorials/ConfigsGeneration.html">Tutorials: Configuration Generation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../Tutorials/ConfigsRelaxation.html">Tutorials: Configuration Relaxation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../Tutorials/ConfigsSelection.html">Tutorials: Configuration Selection</a></li>

diff --git a/docs/OpenNucleome.html b/docs/OpenNucleome.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>openNucleome &mdash; openNucleome 1.1.0 documentation</title><link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  <title>openNucleome &mdash; openNucleome 1.1.3 documentation</title><link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/jupyter-sphinx.css" type="text/css" />
       <link rel="stylesheet" href="_static/thebelab.css" type="text/css" />
@@ -41,7 +41,7 @@
               <img src="_static/website_pic.png" class="logo" alt="Logo"/>
           </a>
               <div class="version">
-                1.1.0
+                1.1.3
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -72,7 +72,7 @@
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="Tutorials/LangevinSimulation.html">Sphere Model: Langevin Dynamics</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Tutorials/BrownianSimulation.html">Sphere Model: Brownian Dynamics</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Tutorials/NuclearDeformation.html">Ellipsoid Model: Nuclear Deformation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Tutorials/NuclearDeformation.html">Nuclear Deformation Simulation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Tutorials/ConfigsGeneration.html">Tutorials: Configuration Generation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Tutorials/ConfigsRelaxation.html">Tutorials: Configuration Relaxation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Tutorials/ConfigsSelection.html">Tutorials: Configuration Selection</a></li>
@@ -500,10 +500,6 @@ <h2>openNucleome.whole_nucleus_model<a class="headerlink" href="#opennucleome-wh
 </dd>
 <dt>N_type (int, required):</dt><dd><p>the number of types in the system.</p>
 </dd>
-<dt>N_chr (int, required):</dt><dd><p>the number of chromosome beads in the system.</p>
-</dd>
-<dt>N_chr_nuc (int, required):</dt><dd><p>the number of chromosome and nucleolus beads in the system.</p>
-</dd>
 <dt>bond_list (list, required):</dt><dd><p>contains the corresponding atom indexes of all bonds.</p>
 </dd>
 <dt>compart_type (list, required):</dt><dd><p>contains the corresponding compartment types of all beads.</p>
@@ -581,8 +577,6 @@ <h2>openNucleome.whole_nucleus_model<a class="headerlink" href="#opennucleome-wh
 </dd>
 <dt>N_type (int, required):</dt><dd><p>the number of types in the system.</p>
 </dd>
-<dt>N_chr_nuc_spec (int, required):</dt><dd><p>the number of chromosome, nucleolus, and the speckle beads in the system.</p>
-</dd>
 <dt>bond_list (list, required):</dt><dd><p>contains the corresponding atom indexes of all bonds.</p>
 </dd>
 <dt>compart_type (list, required):</dt><dd><p>contains the corresponding compartment types of all beads.</p>